Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Micro-PVM"
graph_weight
## [1] "1.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   32.00   36.75   38.00   37.58   39.00   42.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 32 33 34 34 35 35 36 36 36 36 37 37 37 37 37 37 37 37 37 38 38 38 38 38 38
## [26] 38 38 38 39 39 39 40 40 40 40 40 40 41 41 42

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))
## 
## FALSE  TRUE 
##  1739   261
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    21  1718   261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1 
## 2000

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
gene_dat = fread(sprintf("data/%s_genes_info.csv", cell_type_name))
dim(gene_dat)
## [1] 36517     9
gene_dat[1:2,]
##           gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003               FALSE       TSPAN6    NCBITaxon:9606
## 2: ENSG00000000005               FALSE         TNMD    NCBITaxon:9606
##    feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1:            gene                76    0.002350               99.8100
## 2:            gene                 1    0.000025               99.9975
##    total_counts
## 1:           94
## 2:            1
length(unique(gene_info$sym_in_data))
## [1] 2000
table(gene_info$sym_in_data %in% gene_dat$feature_name)
## 
## TRUE 
## 2000
table(gene_dat$feature_name %in% gene_info$sym_in_data)
## 
## FALSE  TRUE 
## 34517  2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1

table(gene_dat$selected)
## 
##     0     1 
## 34517  2000
tapply(gene_dat$pct_dropout_by_counts, gene_dat$selected, summary)
## $`0`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00   94.48   99.58   93.53   99.97  100.00 
## 
## $`1`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data", 
                  by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)
## [1] 2000   12
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol        gene_ids feature_is_filtered
## 1:        AATK      AATK        AATK ENSG00000181409               FALSE
## 2:        ABAT      ABAT        ABAT ENSG00000183044               FALSE
##    feature_reference feature_biotype n_cells_by_counts mean_counts
## 1:    NCBITaxon:9606            gene              3157    0.091525
## 2:    NCBITaxon:9606            gene              9074    0.368950
##    pct_dropout_by_counts total_counts selected
## 1:               92.1075         3661        1
## 2:               77.3150        14758        1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol", 
              bias.data = 100 - gene_info$pct_dropout_by_counts)
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "SYT7"          "CDH20"         "NALCN"         "ARFGEF3"      
##  [5] "ADAM23"        "DNAH6"         "CHD5"          "CSMD2"        
##  [9] "PCSK2"         "ATP8A2"        "CBLN2"         "STXBP5L"      
## [13] "TENM2"         "CNTN5"         "ZNF385D"       "AK5"          
## [17] "CLSTN2"        "ANKRD30BL"     "RANBP3L"       "ADGRV1"       
## [21] "AMER2"         "GREM1"         "FSTL5"         "FUT9"         
## [25] "HPSE2"         "SRRM3"         "SSTR2"         "FLRT2"        
## [29] "CACNA1E"       "LINC00632"     "BASP1-AS1"     "ROR1-AS1"     
## [33] "RP11-191L9.4"  "AC093843.1"    "LINC01435"     "RP11-384F7.2" 
## [37] "CTC-340A15.2"  "SLC5A4-AS1"    "CTC-535M15.2"  "RMST"         
## [41] "RP11-436D23.1"

## [1] 2
##  [1] "PDK4"          "ABCB4"         "CPED1"         "GASK1A"       
##  [5] "SESN3"         "TENM4"         "GASK1B"        "FOLR2"        
##  [9] "ARHGAP42"      "PLD4"          "CYSLTR1"       "C5orf64"      
## [13] "RAB39A"        "CLEC9A"        "MAMDC2-AS1"    "AC003090.1"   
## [17] "LMCD1-AS1"     "HDAC2-AS2"     "LINC02642"     "RP11-634B7.4" 
## [21] "COX10-AS1"     "AC008697.1"    "LINC01301"     "LINC01094"    
## [25] "MAILR"         "MIR3142HG"     "RP11-946L16.1" "RP11-554D14.6"
## [29] "RP11-187O7.3"  "MRC1"          "MIR222HG"      "MIR223HG"     
## [33] "LINC00506"     "RP11-323F24.5" "RP11-685G11.1" "RP11-4F5.3"   
## [37] "CPM"           "KCNE1"

## [1] 3
##  [1] "SIGLEC1"       "ADGRD1"        "F13A1"         "LILRB2"       
##  [5] "ENOSF1"        "IFI44L"        "CH25H"         "FHAD1"        
##  [9] "TMEM163"       "ADAMTS15"      "PGBD5"         "ODF3B"        
## [13] "PLCXD3"        "MS4A4E"        "RP11-445F6.2"  "LINC01515"    
## [17] "AC092431.3"    "LINC02008"     "BDNF-AS"       "LINC02211"    
## [21] "LINC02432"     "C5orf17"       "LINC02196"     "FAM66D"       
## [25] "OVCH1-AS1"     "RP11-72M17.1"  "CTD-2336H13.2" "LINC02073"    
## [29] "RP11-154H12.3" "RP11-354K4.2"  "CCDC28A-AS1"   "LINC01374"    
## [33] "RP11-281A20.2" "CERNA2"        "RP11-221G19.1" "RP11-321P16.3"
## [37] "RP13-52K8.2"

## [1] 4
##  [1] "ACER3"         "CARMIL1"       "SYNDIG1"       "FAM149A"      
##  [5] "TBC1D14"       "NPL"           "NKD1"          "AOPEP"        
##  [9] "DISP1"         "SAMSN1"        "DEPTOR"        "DENND2B"      
## [13] "ATF7IP2"       "TMC7"          "SPTLC3"        "SCAI"         
## [17] "ZDHHC14"       "KCNQ3"         "PRKN"          "RANBP17"      
## [21] "LINC02649"     "MIR99AHG"      "RP1-30E17.2"   "HMGA1P4"      
## [25] "ZFPM2-AS1"     "RP11-10H3.1"   "RP11-692P14.1" "RP6-91H8.6"   
## [29] "ARHGAP6"       "KCNQ2"         "RAP1GAP"       "PILRA"        
## [33] "GRK3"          "PADI2"         "SEC14L1"       "SLC2A13"      
## [37] "KCNQ5"         "LNCAROD"

## [1] 5
##  [1] "MGLL"          "PRTFDC1"       "NIPAL2"        "MAP2K6"       
##  [5] "IFT43"         "CCDC18"        "SSPN"          "GSTCD"        
##  [9] "MED12L"        "FILIP1L"       "GPR34"         "CENPP"        
## [13] "RP5-1132H15.1" "RMDN2-AS1"     "RP11-692D12.1" "LINC00624"    
## [17] "HGF"           "TGFB2"         "TMED8"         "CLNK"         
## [21] "HPCAL1"        "TOX2"          "TMEM115"       "GYPC"         
## [25] "FAM117B"       "CCDC40"        "IQGAP2"        "HTR7"         
## [29] "PARP8"         "PCNT"          "RHOBTB3"       "ABCA1"        
## [33] "GLRX"          "GOLIM4"        "EFCAB2"        "SLC48A1"      
## [37] "SBF2-AS1"      "RP11-154H23.4"

## [1] 6
##  [1] "HHAT"       "ZNF821"     "MOBP"       "AATK"       "ST3GAL1"   
##  [6] "FAM50A"     "RGS1"       "MTMR8"      "ADAP1"      "MEGF9"     
## [11] "SNX25"      "DARS1"      "CDH26"      "SEM1"       "AFDN"      
## [16] "KIAA0513"   "GPNMB"      "CCNG2"      "ARHGAP18"   "TIAM2"     
## [21] "RSU1"       "FRRS1"      "ABCG1"      "ANKZF1"     "MARCHF8"   
## [26] "APLF"       "MFSD4B"     "ZC3H6"      "DPYD"       "PARVB"     
## [31] "H1-0"       "CYRIA"      "GCC2-AS1"   "AC093818.1" "PIK3IP1-DT"
## [36] "MIR181A1HG" "IFITM10"    "CLEC5A"

## [1] 7
##  [1] "SLC4A7"   "EPB41L2"  "POLA1"    "TGFBR1"   "SIPA1L2"  "BIN1"    
##  [7] "BACH1"    "SOCS6"    "SH3RF3"   "FNDC3B"   "TRIP11"   "TJP1"    
## [13] "ARHGEF10" "DDX5"     "GAB1"     "E2F3"     "P4HA1"    "RASSF8"  
## [19] "RUNX2"    "ARHGAP22" "UACA"     "FNBP1L"   "MSN"      "MCPH1"   
## [25] "MGAT5"    "RUNX1"    "ZNF143"   "AXL"      "LDLRAD4"  "ALCAM"   
## [31] "PEAK1"    "SND1"

## [1] 8
##  [1] "PDE10A"        "GNLY"          "ADAMTS19"      "GLT1D1"       
##  [5] "BANK1"         "ADAMTS3"       "UCN"           "MT1E"         
##  [9] "TMEM151B"      "RFLNA"         "ZNF804B"       "LINC01277"    
## [13] "AC073115.7"    "AC002539.1"    "RP3-525N10.2"  "LINC00271"    
## [17] "KIF5C-AS1"     "LINC02884"     "AC007682.1"    "AC073115.6"   
## [21] "MIR4300HG"     "STARD4-AS1"    "LINC00923"     "LINC02055"    
## [25] "RP4-809F18.1"  "MTRNR2L8"      "LINC02316"     "PSMD7-DT"     
## [29] "RP11-621L6.2"  "RP11-58G13.1"  "RP11-413N10.3" "RP11-640F22.1"
## [33] "LINC02885"     "RP11-38B6.1"   "RP11-320L2.1"  "RP11-341N18.1"

## [1] 9
##  [1] "HTR2B"     "PNMA3"     "ZNRF1"     "NFIX"      "NSMAF"     "PDE8A"    
##  [7] "GRAMD4"    "FOSL2"     "TBC1D2"    "PCSK5"     "RNF24"     "BNIP3L"   
## [13] "GYS1"      "PPARD"     "PFKFB4"    "GBE1"      "PAPOLG"    "NR4A3"    
## [19] "ATF1"      "KDM6B"     "PHF21A"    "GLUL"      "GABARAPL1" "PELI2"    
## [25] "GNA12"     "SLC25A37"  "ARID5B"    "CFDP1"     "MAPK13"    "SPRY1"    
## [31] "NFIL3"     "PPIP5K1"   "KLHL6"     "PPP1R3B"   "BNIP3"     "TRNAU1AP" 
## [37] "LIMK2"

## [1] 10
##  [1] "SCMH1"                   "KIFAP3"                 
##  [3] "APBB1IP"                 "TMEM156"                
##  [5] "SPATA6"                  "FRMD6"                  
##  [7] "KCNMB1"                  "RASGEF1C"               
##  [9] "KCNMA1"                  "AUTS2"                  
## [11] "TAGAP"                   "TMEM52B"                
## [13] "NAV2"                    "ZNF608"                 
## [15] "TLN2"                    "GAP43"                  
## [17] "OLR1"                    "DLEU1"                  
## [19] "B3GNT5"                  "NCKAP5"                 
## [21] "SPATA13_ENSG00000182957" "SLC8A1"                 
## [23] "SFMBT2"                  "MBD5"                   
## [25] "TMSB4X"                  "LTC4S"                  
## [27] "RP11-557H15.4"           "LINC02232"              
## [29] "RP11-419I17.1"           "RNASET2"                
## [31] "RGCC"                    "ZBTB46"                 
## [33] "PCGF5"                   "FMN1"

## [1] 11
##  [1] "MUSK"                      "EFR3B"                    
##  [3] "PROCR"                     "CRYM"                     
##  [5] "STMN2"                     "ECM2"                     
##  [7] "OPRM1"                     "PODXL2"                   
##  [9] "NEK11"                     "WLS"                      
## [11] "IFIT3"                     "IFIT2"                    
## [13] "FMO5"                      "ABCA8"                    
## [15] "MMS22L"                    "IER2"                     
## [17] "FAM227B"                   "BEAN1"                    
## [19] "GLYATL1"                   "MYO5B"                    
## [21] "SLC35G2"                   "CPLX1"                    
## [23] "DTWD2"                     "DENND5B"                  
## [25] "GRIK1"                     "PC"                       
## [27] "MCMDC2"                    "TSPYL2"                   
## [29] "IFIT1"                     "STMN3"                    
## [31] "H2BC18"                    "SMCR5"                    
## [33] "GPRC5D-AS1"                "LINC01605_ENSG00000253161"
## [35] "RP11-867G2.8"              "RP11-314L11.1"            
## [37] "TMEM140"

## [1] 12
##  [1] "PLPP1"          "HAMP"           "AZIN2"          "SHOC1"         
##  [5] "NLGN4Y"         "MICOS10"        "ADGRG2"         "TTTY14"        
##  [9] "FLJ40194"       "DLEU7"          "COL25A1"        "EDNRB-AS1"     
## [13] "ENTPD1-AS1"     "SLC8A1-AS1"     "RP11-202G18.1"  "HCG22"         
## [17] "CCDC26"         "RP11-142M10.2"  "LINC00884"      "RNASEH2B-AS1"  
## [21] "RP11-353M9.1"   "CCDC200"        "RP11-360F5.1"   "LINC02057"     
## [25] "LINC01258"      "RP11-238K6.1"   "RP11-624C23.1"  "RP11-452H21.1" 
## [29] "SMIM35"         "RP11-196H14.2"  "RP11-136F16.1"  "LINC00621"     
## [33] "CEACAM16-AS1"   "RP11-399K21.11" "LINC02712"      "RP11-323P17.2" 
## [37] "RP11-264E23.4"  "RP11-13J12.3"

## [1] 13
##  [1] "ATP8B1"         "SLC5A9"         "SGCE"           "PDE5A"         
##  [5] "ENO4"           "FAM177B"        "INSYN2B"        "ANKUB1"        
##  [9] "AC002463.3"     "ARHGAP26-AS1"   "AC017101.10"    "AC096558.1"    
## [13] "SRGAP2-AS1"     "AC083884.8"     "AC037445.1"     "RP11-666F17.1" 
## [17] "CPB2-AS1"       "MYCBP2-AS1"     "DIAPH2-AS1"     "AC018890.6"    
## [21] "CTD-2015H6.3"   "CTD-2227I18.1"  "RHOQ-AS1"       "RP11-649G15.2" 
## [25] "AP000487.6"     "RP11-513G19.1"  "USP3-AS1"       "RP11-815J21.4" 
## [29] "RP11-16B9.1"    "ABHD15-AS1"     "RP11-16C1.3"    "RP11-793A3.2"  
## [33] "RP11-53B2.3"    "CTD-2282P23.2"  "RP11-793H13.14" "DISC2"         
## [37] "RP11-65F13.4"   "RP11-1146N6.3"  "AC009505.4"

## [1] 14
##  [1] "ZFP64"          "NEXMIF"         "CASS4"          "PITPNM2"       
##  [5] "PLCL1"          "BEX1"           "RALGPS1"        "GPAT3"         
##  [9] "RAB40B"         "NRGN"           "TSPAN7"         "PLXDC1"        
## [13] "SMIM14"         "NXN"            "MIR31HG"        "MACROD2"       
## [17] "FIGN"           "LIPE-AS1"       "ALOX12-AS1"     "KIF9-AS1"      
## [21] "RP11-120D5.1"   "RP11-246A10.1"  "MRPS30-DT"      "RP11-370I10.6" 
## [25] "LINC01572"      "RP11-495L19.1"  "TENM1"          "ADGRL1"        
## [29] "GDF11"          "PLXNC1"         "CFAP161"        "ST3GAL2"       
## [33] "CXXC5"          "CDH4"           "ANKS1B"         "CTD-3088G3.8"  
## [37] "SYCP2"          "RORB"           "LL22NC03-2H8.5"

## [1] 15
##  [1] "ADAM28"      "ST6GAL1"     "IPCEF1"      "PLAT"        "IGSF21"     
##  [6] "RCAN3"       "PLAU"        "ITPR2"       "ABCC4"       "C3"         
## [11] "FOXP2"       "LYVE1"       "GARNL3"      "GIPC2"       "GAREM1"     
## [16] "AIG1"        "FRMD4A"      "PRMT9"       "CX3CR1"      "P2RY12"     
## [21] "LRRC8C"      "CA8"         "SLC9A9"      "CH17-55D9.1" "ARHGAP15"   
## [26] "SLC1A3"      "IL27RA"      "LIFR"        "FOXP1"       "OGFRL1"     
## [31] "SLC41A2"     "CSGALNACT1"  "JAZF1"       "MTSS1"       "BNC2"       
## [36] "MAML2"       "IFNLR1"

## [1] 16
##  [1] "HIVEP2"        "SLC9A7"        "HDHD5"         "MAP3K20"      
##  [5] "ARRDC2"        "AK1"           "STN1"          "MXI1"         
##  [9] "GTDC1"         "ATP8A1"        "CEMIP2"        "RASGEF1B"     
## [13] "PGGHG"         "ST18"          "SLC26A7"       "ZFYVE28"      
## [17] "KLF13"         "RESF1"         "LPCAT4"        "RBM44"        
## [21] "TMTC2"         "TNFAIP8L3"     "NCMAP"         "ZNF395"       
## [25] "TPRG1"         "ERO1A"         "LINC02397"     "AS3MT"        
## [29] "FAM229A"       "SGO1-AS1"      "DIRC3"         "DARS1-AS1"    
## [33] "LINC01762"     "AF064858.8"    "RP11-305L7.3"  "FMNL1-DT"     
## [37] "LINC01138"     "MYOCOS"        "RP11-344F5.1"  "RP11-249L21.6"

## [1] 17
##  [1] "MMP24"         "GLIPR1L1"      "EYS"           "FSIP2"        
##  [5] "SPDYE2"        "HDAC4-AS1"     "ELMO1-AS1"     "TMLHE-AS1"    
##  [9] "HNRNPA1P48"    "LINC01375"     "AC105461.1"    "RP11-165F24.3"
## [13] "RP11-526K17.2" "ALG13-AS1"     "RP1-225E12.2"  "COA6-AS1"     
## [17] "RP11-528G1.2"  "RP11-575L7.8"  "BCL2L1-AS1"    "DENND6A-AS1"  
## [21] "ZBTB20-AS5"    "LINC00960"     "RP11-712B9.2"  "MEF2C-AS2"    
## [25] "RP11-268P4.5"  "RP11-39E3.3"   "RP11-506H20.1" "RP11-434H14.1"
## [29] "RP11-370I10.2" "CTD-2647E9.3"  "RP11-317G6.1"  "RP11-703M24.5"
## [33] "CTD-3149D2.4"  "RP4-769N13.7"  "RP1-256G22.2"  "RP11-121C2.3" 
## [37] "RP11-7F3.1"    "RP11-685G9.5"  "RP11-555K12.4" "RP11-56I23.2"

## [1] 18
##  [1] "ZFY"                     "SLC26A3"                
##  [3] "PCDH11Y"                 "PXDNL"                  
##  [5] "NR6A1"                   "SEMA3E"                 
##  [7] "FUT10"                   "LRRC3B"                 
##  [9] "CCDC73"                  "POTEG"                  
## [11] "RP11-37N22.1"            "AC023469.1"             
## [13] "AC067959.1"              "RP11-147G16.1"          
## [15] "RP11-154D17.1"           "MYO16-AS1"              
## [17] "AC013463.2"              "LINC02646"              
## [19] "AC002066.1"              "CTD-2643I7.5"           
## [21] "RP11-696N14.1"           "RP11-17A1.3"            
## [23] "RP11-259O2.1"            "RP11-79E3.2"            
## [25] "LINC01609"               "RP11-351A11.1"          
## [27] "RP11-13N12.1"            "RP11-20D14.3"           
## [29] "MTRNR2L12"               "RMRP_ENSG00000269900"   
## [31] "SCARNA2_ENSG00000270066" "AGBL1"                  
## [33] "CH507-513H4.1"           "CH507-528H12.1"         
## [35] "RP11-596C23.6"           "RP4-799O8.1"            
## [37] "RP11-322M13.1"           "AC003099.2"             
## [39] "RP11-398J12.1"           "RP11-404C6.6"

## [1] 19
##  [1] "RPL3"          "RPL18A"        "RPL19"         "RPL34"        
##  [5] "RPL24"         "FGF13"         "MTHFS"         "RPS24"        
##  [9] "PRDM5"         "RPS2"          "RPS11"         "RPL11"        
## [13] "SPAG16"        "RPL32"         "FAU"           "ATG10"        
## [17] "RPL26"         "ELAVL4"        "MRPL1"         "RPL38"        
## [21] "RPLP2"         "RPS23"         "SPATS2L"       "CPNE4"        
## [25] "RPL12"         "RPL23A"        "RPL39"         "AIF1"         
## [29] "RP11-535M15.1" "LINC01278"     "PVT1"          "RP11-37B2.1"  
## [33] "SLC1A2"        "LPL"           "ADARB1"        "LILRB3"

## [1] 20
##  [1] "STS"        "MID1"       "CCDC170"    "DOCK10"     "IRF8"      
##  [6] "ITGA9"      "AC097721.2" "XIST"       "TWIST2"     "MEI4"      
## [11] "SCIN"       "LCP2"       "CTTNBP2"    "DOCK9"      "IRAK3"     
## [16] "INTS6"      "NCOA7"      "TSHZ3"      "PTPRE"      "PRAM1"     
## [21] "CCNH"       "FAM13A"     "SSH2"       "USP53"      "SDK1"      
## [26] "DIXDC1"     "FER"        "ACSL1"      "MERTK"      "GPHN"      
## [31] "CHD2"       "CMSS1"      "GPRIN3"     "MITF"       "RALGAPA2"  
## [36] "PLCG2"

## [1] 21
##  [1] "MPP2"     "ATF5"     "FGR"      "LRRC7"    "CDK14"    "CDK17"   
##  [7] "ARHGAP10" "IGSF9B"   "ITPKC"    "HIVEP1"   "FGF14"    "POU6F2"  
## [13] "CPE"      "MOB3B"    "RAMP1"    "MACROD1"  "PDZD2"    "CNKSR2"  
## [19] "ADGRL3"   "LONRF1"   "NCAM2"    "SORCS3"   "GMEB1"    "CSMD3"   
## [25] "CRADD"    "NLGN1"    "CTNND2"   "PTGER4"   "NEGR1"    "CNTNAP2" 
## [31] "CADM2"    "ZBTB7A"   "NRXN1"    "ZBTB7C"   "LSAMP"    "NRG3"    
## [37] "SNHG14"

## [1] 22
##  [1] "ICA1"         "MCF2L2"       "IL1A"         "ZRANB3"       "EFCAB11"     
##  [6] "TCERG1L"      "KCNMB2"       "CTA-292E10.6" "LINC00996"    "KCNQ1OT1"    
## [11] "AC009166.9"   "CNTN1"        "NCDN"         "HPCAL4"       "SLC2A5"      
## [16] "CACNA1B"      "CACNA1C"      "SCN3A"        "CACNA2D1"     "PTPRN2"      
## [21] "SYN2"         "SPTBN4"       "EDIL3"        "RBFOX3"       "GRM5"        
## [26] "KCND3"        "DPP10"        "MSRA"         "PCDH9"        "KCND2"       
## [31] "PRKG1"        "SYN3"         "GRM7"         "FAM153CP"     "U91319.1"

## [1] 23
##  [1] "CEACAM1"       "SLC9B1"        "RP11-281P23.2" "RP11-493L12.3"
##  [5] "RP11-516C1.1"  "CELSR3"        "ABCA7"         "PLEKHH3"      
##  [9] "ANO8"          "MLF2"          "GALNT16"       "HELLS"        
## [13] "TGFBI"         "HIF3A"         "CHI3L1"        "FGF17"        
## [17] "LYPD5"         "TNFRSF11B"     "ADCY5"         "H2AC6"        
## [21] "VMO1"          "NHEJ1"         "EME2"          "ZNF521"       
## [25] "ZDBF2"         "AF064858.6"    "SLC12A8"       "RP11-384C4.7" 
## [29] "RP3-467L1.4"   "RP11-657O9.1"  "ARHGEF25"      "LINC01414"    
## [33] "RP11-661A12.5" "MTRNR2L1"      "RP11-429A20.3" "RP11-81K2.1"  
## [37] "LINC00551"

## [1] 24
##  [1] "ZDHHC19"       "RP11-713N11.4" "PKD1"          "SLC2A3"       
##  [5] "DDX3Y"         "HACE1"         "PPP1R15A"      "GADD45B"      
##  [9] "RNMT"          "FLT1"          "IL4I1"         "APBB3"        
## [13] "USP9Y"         "SPP1"          "SRGN"          "TREM1"        
## [17] "MICAL2"        "RGS16"         "MYO10"         "PLIN2"        
## [21] "TAMALIN"       "ALDH1A1"       "DDIT4"         "FAM210A"      
## [25] "ADSS1"         "ANKRD37"       "IARS1"         "H2BU1"        
## [29] "CEBPD"         "ZSCAN31"       "HIF1A-AS3"     "CTD-2285E13.1"
## [33] "RP11-134L10.2"

## [1] 25
##  [1] "CALCR"         "IL7"           "NEURL2"        "PIGC"         
##  [5] "ADGRA3"        "ADGRG5"        "RNF180"        "LINC00476"    
##  [9] "IRAG1-AS1"     "CATSPERE"      "SDHAF3"        "SCOC-AS1"     
## [13] "PAPSS2"        "CARNMT1-AS1"   "ATP6AP1L"      "ENTPD3-AS1"   
## [17] "TMEM72-AS1"    "TSBP1-AS1"     "RP13-188A5.1"  "RP5-1198O20.4"
## [21] "FSIP2-AS1"     "IPO9-AS1"      "UFL1-AS1"      "RPL34-DT"     
## [25] "RP11-195C7.1"  "LRIG2-DT"      "LINC01877"     "RORA-AS1"     
## [29] "STX18-AS1"     "RP11-130F10.1" "LIX1-AS1"      "DISC1FP1"     
## [33] "RP11-160E2.6"  "RP11-74J13.8"  "EIF1B-AS1"     "RP11-736I24.5"
## [37] "RP11-19D22.1"  "RP11-622O11.6" "RP11-261A24.1" "RP11-237N2.1" 
## [41] "RP1-236J16.3"  "RP11-120L14.1"

## [1] 26
##  [1] "ERCC8"         "DHRS9"         "ANGPT2"        "CHN1"         
##  [5] "UBE2Q2"        "BCL2A1"        "TNFRSF21"      "IRAK1BP1"     
##  [9] "TEX9"          "ABCA5"         "PAQR3"         "LCLAT1"       
## [13] "RP11-131L23.1" "RPL41"         "VCAN"          "KCNAB2"       
## [17] "MYOM1"         "KATNAL1"       "SPOCK2"        "SLC16A10"     
## [21] "GABRG2"        "CYTIP"         "HIP1"          "BTG1"         
## [25] "PITPNC1"       "RASA2"         "ZMAT4"         "OTUD1"        
## [29] "ATOH8"         "C11orf80"      "MCTP1"         "JAKMIP2"      
## [33] "CD247"         "TOX"           "MIR155HG"      "LUCAT1"       
## [37] "RP11-475M20.2"

## [1] 27
##  [1] "DERA"     "TDRD3"    "DAAM1"    "GDAP1"    "ARSB"     "EPHB2"   
##  [7] "STAMBPL1" "NUBPL"    "NFIA"     "KIF26B"   "ARHGAP25" "DYNC2H1" 
## [13] "CCDC7"    "CLEC16A"  "LIMCH1"   "RFX3"     "PHLPP1"   "RFX2"    
## [19] "TRPS1"    "PRKAG2"   "SASH1"    "ELL2"     "IQSEC2"   "IQSEC1"  
## [25] "FARP1"    "MSI2"     "RBM47"    "SLC43A2"  "DHRSX"    "AFF1"    
## [31] "PACS1"    "SAMD12"   "SERTAD2"  "GDI1"

## [1] 28
##  [1] "RIPOR2"        "DUOX1"         "MCTP2"         "TMEM44"       
##  [5] "LINC00467"     "BEX3"          "RAB37"         "H2BC4"        
##  [9] "H2AC20"        "MTCP1"         "GOLGA8B"       "AC023590.1"   
## [13] "ZNF451-AS1"    "WEE2-AS1"      "PCDH9-AS2"     "RP11-142A5.1" 
## [17] "KCNMA1-AS1"    "RP11-544A12.4" "RP5-1101C3.1"  "RP11-115J16.1"
## [21] "RP11-120A1.1"  "RP11-463D19.1" "RP11-511B23.2" "RP1-71H24.1"  
## [25] "TCF4-AS1"      "RP11-126O1.4"  "TSIX"          "H2AC19"       
## [29] "RP11-386I14.4" "H2BC8"         "H2AC8"         "H2BC7"        
## [33] "TRG-AS1"       "RP11-275G7.2"  "GS1-98E2.1"    "RP11-21M24.6" 
## [37] "RP11-314E10.1" "RP11-399K19.1" "NIBAN2"

## [1] 29
##  [1] "CD74"          "CST3"          "OGN"           "SLC2A9"       
##  [5] "FLVCR2"        "XAF1"          "ITM2C"         "SMAD6"        
##  [9] "PTH2R"         "LY96"          "COPG2"         "C1QC"         
## [13] "S100Z"         "C1QB"          "RTTN"          "PROS1"        
## [17] "CHSY3"         "FIRRE"         "LINC00894"     "RP11-574F11.4"
## [21] "TRHDE"         "RASSF2"        "MAN1A1"        "FRMD4B"       
## [25] "COL5A1"        "CHSY1"         "TLR2"          "NGLY1"        
## [29] "CDCP1"         "NPTX1"         "LRFN4"         "TLR5"         
## [33] "PELI1"         "GK"            "ZNF277"        "UBXN2B"       
## [37] "ZNF407"

## [1] 30
##  [1] "PRDM11"        "CFAP74"        "RTN4RL1"       "KCNT1"        
##  [5] "BICRAL"        "SEMA6D"        "ZNF365"        "RBMS3"        
##  [9] "NPAS3"         "SPOCK1"        "CFAP251"       "CAMK2N1"      
## [13] "GABRB1"        "LRFN5"         "PDZRN4"        "HTR1E"        
## [17] "GPC5"          "KCTD16"        "GLDN"          "PTPRT"        
## [21] "NPIPB15"       "ZNF846"        "TAFA2"         "FAM155A"      
## [25] "MEG3"          "MIAT"          "RP5-864K19.4"  "ARL17B"       
## [29] "SHISA9"        "RP11-111A21.1" "RP11-707P17.1" "RP11-368L12.1"
## [33] "RP11-396B14.2" "IQCJ-SCHIP1"   "RP11-114N19.3" "RP11-358F13.1"
## [37] "RP11-335E8.3"  "RP11-452F19.4"

## [1] 31
##  [1] "TTC7A"         "SP140"         "ARHGEF18"      "TMEM241"      
##  [5] "ARL5C"         "BEND6"         "ENPP3"         "C4orf19"      
##  [9] "MAMDC2"        "LIPC"          "ZMAT3"         "MARCHF3"      
## [13] "SCFD2"         "CDIN1"         "KBTBD12"       "LINC01356"    
## [17] "LINC01357"     "LINC00539"     "AC105760.2"    "LINC01141"    
## [21] "LINC01684"     "KCNMB2-AS1"    "ARHGAP8"       "XACT"         
## [25] "PTCHD4"        "LINC00968"     "MEF2C-AS1"     "RP11-541P9.3" 
## [29] "ZNF10"         "RP11-630C16.2" "RP11-493L12.4" "LINC00907"    
## [33] "ATP6V0D1-DT"   "RP11-437L7.2"  "RP11-111G13.1" "RP4-545L17.11"
## [37] "RP11-168F24.3" "STAB1"         "AC025171.1"    "CTB-41I6.2"

## [1] 32
##  [1] "ZNF532"       "OPHN1"        "PIGL"         "MS4A4A"       "TENT5A"      
##  [6] "LDAH"         "MTERF1"       "PUDP"         "SLC49A4"      "FBN2"        
## [11] "WDPCP"        "PID1"         "CLIC2"        "RAB28"        "NMNAT3"      
## [16] "TMEM144"      "CCDC171"      "ACYP2"        "FGGY"         "WDR25"       
## [21] "PCED1B"       "RNLS"         "B3GLCT"       "LINC01285"    "PRDX6-AS1"   
## [26] "ZNF433-AS1"   "FTCDNL1"      "SLC16A1-AS1"  "TEX41"        "ZRANB2-AS2"  
## [31] "RFX3-AS1"     "LINC01376"    "LINC01184"    "RP11-319G6.1" "CTB-161M19.4"
## [36] "C8orf37-AS1"  "PRANCR"       "LINC01146"    "MMP28"        "RP1-111C20.3"

## [1] 33
##  [1] "OSBPL6"   "PDE4D"    "RALGPS2"  "RFC3"     "PIGK"     "MAGI1"   
##  [7] "PTPN14"   "SETBP1"   "TIAM1"    "PLEKHA7"  "ATAD5"    "DNAH14"  
## [13] "WWC3"     "PLEKHA5"  "PDE4A"    "CUX2"     "RLF"      "ESYT2"   
## [19] "DENND1A"  "MAPK8IP1" "STARD13"  "AGAP3"    "DENND4C"  "WDR45B"  
## [25] "RIT2"     "SRSF12"   "AGAP1"    "FAM110B"  "ROBO1"    "TANC2"   
## [31] "FAM20C"   "CADM1"    "PDE4B"    "SIPA1L1"  "RGL3"

## [1] 34
##  [1] "TXNDC16"                 "PCSK1N"                 
##  [3] "LRRC6"                   "CALY"                   
##  [5] "LPAR6"                   "UNC80"                  
##  [7] "GPR85"                   "SKA2"                   
##  [9] "ERC2"                    "COL5A2"                 
## [11] "AC011288.2"              "ALG1L9P_ENSG00000248671"
## [13] "CTD-2537O9.1"            "CEROX1"                 
## [15] "RP11-305E17.8"           "COPG2IT1"               
## [17] "ADAM22"                  "RAPGEF4"                
## [19] "ANKRD12"                 "RAPGEF1"                
## [21] "PPFIA2"                  "CDH18"                  
## [23] "FMN2"                    "FMNL2"                  
## [25] "CLASP2"                  "OXR1"                   
## [27] "LRP1B"                   "DLGAP1"                 
## [29] "RIMS2"                   "CSMD1"                  
## [31] "OPCML"                   "RALYL"                  
## [33] "KCNIP4"                  "MYT1L"                  
## [35] "MAGI2"                   "COL27A1"                
## [37] "NEAT1"                   "SAP30-DT"

## [1] 35
##  [1] "PRKCQ"        "MTHFD2L"      "PRKCH"        "ARAP2"        "ZFAT"        
##  [6] "MYO9A"        "SESN1"        "ZNF586"       "DOCK3"        "DCUN1D4"     
## [11] "WNT2B"        "RGL1"         "CAMKMT"       "AMN1"         "RASGRP3"     
## [16] "AGPAT5"       "ADK"          "CDC42SE2"     "EPB41"        "STARD9"      
## [21] "NEK10"        "RNF150"       "MALT1"        "SLC35E3"      "ZHX2"        
## [26] "AIDA"         "ARL4C"        "CARD11"       "LINC00862"    "DENND1B"     
## [31] "C17orf67"     "SOGA3"        "KLF3-AS1"     "AC092835.2"   "RP1-179N16.6"
## [36] "SELENOP"      "HCG17"        "C2orf27A"

## [1] 36
##  [1] "MBNL3"         "P3H2"          "APBA1"         "GCNT2"        
##  [5] "PEX7"          "AKAP7"         "SLC10A7"       "RAB38"        
##  [9] "DTD1"          "METTL25"       "LANCL2"        "DPH6"         
## [13] "ARHGAP20"      "ARMH4"         "LRIG1"         "CD226"        
## [17] "MAP3K7CL"      "TNFRSF13C"     "PUS10"         "MBOAT1"       
## [21] "CAPS2"         "LEKR1"         "LIN52"         "LINC00630"    
## [25] "RP11-162D16.2" "MIR646HG"      "C12orf75"      "RP11-381K20.2"
## [29] "LINC02762"     "GMDS-DT"       "RP11-679C8.2"  "LINC02328"    
## [33] "RP11-323I15.5" "KLHL24"        "SLC35E1"       "IL15"         
## [37] "TMEM65"

## [1] 37
##  [1] "SLC26A4"    "PLGRKT"     "MAP3K8"     "PLEK"       "CENPK"     
##  [6] "MIS18BP1"   "SAT1"       "ZSCAN5A"    "PCBD2"      "EPSTI1"    
## [11] "AHI1"       "SLC22A23"   "BCAS3"      "TRPC1"      "SLC25A25"  
## [16] "C11orf49"   "PSTPIP2"    "CACNA1D"    "BTG2"       "ANO10"     
## [21] "CDYL2"      "PBX3"       "XKR6"       "MX2"        "APOO"      
## [26] "KIAA0825"   "ZFP36L1"    "SRGAP3"     "CDKN2B-AS1" "JARID2"    
## [31] "MSR1"       "CTNNA2"     "UBE2R2"     "MGAT1"      "RNF144B"   
## [36] "TNFAIP8"    "RASSF3"     "ACOT11"

## [1] 38
##  [1] "SNCAIP"  "RPH3A"   "LRRC74A" "MEIS1"   "RORA"    "RAB27A"  "SMARCD3"
##  [8] "CELF4"   "TBL1X"   "NPDC1"   "EPHA4"   "AKT3"    "EMILIN2" "DRAM1"  
## [15] "KCNH1"   "PAM"     "CLVS2"   "LRRC4C"  "CLEC1A"  "CRIM1"   "PDE3B"  
## [22] "KALRN"   "ZFPM2"   "PPM1E"   "ALOX15B" "ZDHHC20" "UNC5C"   "TSHZ2"  
## [29] "EFNA5"   "NELL2"   "OSBP2"   "PBX1"    "KAZN"    "MIB2"    "MICAL3" 
## [36] "GRIN2B"

## [1] 39
##  [1] "PKD2L2"        "ANGPTL1"       "CYREN"         "ATP5F1E"      
##  [5] "OMD"           "ACKR4"         "IER3"          "AGBL3"        
##  [9] "C11orf65"      "CYTL1"         "DNAJC24"       "RP11-321C24.1"
## [13] "RP4-568F9.6"   "ARHGAP15-AS1"  "RAP2C-AS1"     "LANCL1-AS1"   
## [17] "ITGA9-AS1"     "FBXO30-DT"     "RP11-123B3.2"  "RP1-117O3.2"  
## [21] "KDM4A-AS1"     "RP11-775D22.3" "RP11-796E2.4"  "RP11-544A12.8"
## [25] "ANK2-AS1"      "FAM198B-AS1"   "AC006160.5"    "CTD-3239E11.2"
## [29] "RP11-1H15.2"   "RP11-571M6.7"  "RP11-638I2.8"  "RP11-66H6.3"  
## [33] "PRKCA-AS1"     "RP11-737O24.2" "RP11-622I12.1" "RP11-458A7.1" 
## [37] "RP1-80B9.4"    "RP11-1H15.4"   "RP1-18C9.3"    "RP11-6G22.1"  
## [41] "CTD-2021K4.2"

## [1] 40
##  [1] "ARSJ"          "LINC00639"     "RP11-617F9.2"  "MAMLD1"       
##  [5] "RASGRP2"       "COL5A3"        "LILRB5"        "HS3ST2"       
##  [9] "OLFM1"         "PATJ"          "BTBD11"        "ME3"          
## [13] "FBXO32"        "PALM2AKAP2"    "NRG2"          "JAML"         
## [17] "PLPP3"         "SNED1"         "PRICKLE2"      "ARHGEF3"      
## [21] "STXBP6"        "TBC1D10C"      "ADGRB1"        "H1-10"        
## [25] "SLIT1"         "LINC00910"     "CR1L"          "LINC00970"    
## [29] "XKR9"          "LINC01320"     "SATB1-AS1"     "LIMD1-AS1"    
## [33] "RP11-47I22.3"  "CYP1B1-AS1"    "TRHDE-AS1"     "LINC01322"    
## [37] "USP2-AS1"      "CPEB2-DT"      "RP5-1015P16.1" "RENO1"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_15"
##  [1] "ADAM28"      "ST6GAL1"     "IPCEF1"      "PLAT"        "IGSF21"     
##  [6] "RCAN3"       "PLAU"        "ITPR2"       "ABCC4"       "C3"         
## [11] "FOXP2"       "LYVE1"       "GARNL3"      "GIPC2"       "GAREM1"     
## [16] "AIG1"        "FRMD4A"      "PRMT9"       "CX3CR1"      "P2RY12"     
## [21] "LRRC8C"      "CA8"         "SLC9A9"      "CH17-55D9.1" "ARHGAP15"   
## [26] "SLC1A3"      "IL27RA"      "LIFR"        "FOXP1"       "OGFRL1"     
## [31] "SLC41A2"     "CSGALNACT1"  "JAZF1"       "MTSS1"       "BNC2"       
## [36] "MAML2"       "IFNLR1"     
## $reactome
##                       category over_represented_pvalue under_represented_pvalue
## 241 dissolution of fibrin clot             3.91158e-05                        1
##     numDEInCat numInCat        FDR
## 241          2        3 0.04623487
## 
## [1] "set_19"
##  [1] "RPL3"          "RPL18A"        "RPL19"         "RPL34"        
##  [5] "RPL24"         "FGF13"         "MTHFS"         "RPS24"        
##  [9] "PRDM5"         "RPS2"          "RPS11"         "RPL11"        
## [13] "SPAG16"        "RPL32"         "FAU"           "ATG10"        
## [17] "RPL26"         "ELAVL4"        "MRPL1"         "RPL38"        
## [21] "RPLP2"         "RPS23"         "SPATS2L"       "CPNE4"        
## [25] "RPL12"         "RPL23A"        "RPL39"         "AIF1"         
## [29] "RP11-535M15.1" "LINC01278"     "PVT1"          "RP11-37B2.1"  
## [33] "SLC1A2"        "LPL"           "ADARB1"        "LILRB3"       
## $reactome
##                                              category over_represented_pvalue
## 138                   cellular response to starvation                       0
## 301                 eukaryotic translation elongation                       0
## 302                 eukaryotic translation initiation                       0
## 452                               influenza infection                       0
## 557         metabolism of amino acids and derivatives                       0
## 640                       nonsense mediated decay nmd                       0
## 801       regulation of expression of slits and robos                       0
## 850 response of eif2ak4 gcn2 to amino acid deficiency                       0
## 901                                   rrna processing                       0
## 927                       selenoamino acid metabolism                       0
##     under_represented_pvalue numDEInCat numInCat FDR
## 138                        1         18       26   0
## 301                        1         18       23   0
## 302                        1         18       23   0
## 452                        1         18       27   0
## 557                        1         18       41   0
## 640                        1         18       23   0
## 801                        1         18       27   0
## 850                        1         18       25   0
## 901                        1         18       25   0
## 927                        1         18       26   0
## 
## $go_bp
##                                category over_represented_pvalue
## 630             cytoplasmic translation            0.000000e+00
## 4283                ribosome biogenesis            7.430974e-11
## 4279 ribosomal large subunit biogenesis            7.825622e-09
## 4278   ribosomal large subunit assembly            3.486725e-07
## 4281 ribosomal small subunit biogenesis            1.679751e-06
## 4282                  ribosome assembly            1.700370e-06
## 3144   protein rna complex organization            6.151118e-05
##      under_represented_pvalue numDEInCat numInCat          FDR
## 630                 1.0000000         18       23 0.000000e+00
## 4283                1.0000000          8       13 1.753710e-07
## 4279                1.0000000          5        5 1.231231e-05
## 4278                1.0000000          4        4 4.114336e-04
## 4281                1.0000000          4        5 1.337624e-03
## 4282                1.0000000          4        5 1.337624e-03
## 3144                0.9999984          4       10 4.147611e-02
## 
## [1] "set_28"
##  [1] "RIPOR2"        "DUOX1"         "MCTP2"         "TMEM44"       
##  [5] "LINC00467"     "BEX3"          "RAB37"         "H2BC4"        
##  [9] "H2AC20"        "MTCP1"         "GOLGA8B"       "AC023590.1"   
## [13] "ZNF451-AS1"    "WEE2-AS1"      "PCDH9-AS2"     "RP11-142A5.1" 
## [17] "KCNMA1-AS1"    "RP11-544A12.4" "RP5-1101C3.1"  "RP11-115J16.1"
## [21] "RP11-120A1.1"  "RP11-463D19.1" "RP11-511B23.2" "RP1-71H24.1"  
## [25] "TCF4-AS1"      "RP11-126O1.4"  "TSIX"          "H2AC19"       
## [29] "RP11-386I14.4" "H2BC8"         "H2AC8"         "H2BC7"        
## [33] "TRG-AS1"       "RP11-275G7.2"  "GS1-98E2.1"    "RP11-21M24.6" 
## [37] "RP11-314E10.1" "RP11-399K19.1" "NIBAN2"       
## $reactome
##                                                                               category
## 9    activated pkn1 stimulates transcription of ar androgen receptor regulated genes k
## 76                            assembly of the orc complex at the origin of replication
## 89                                              base excision repair ap site formation
## 247                                                                    dna methylation
## 293                        ercc6 csb and ehmt2 g9a positively regulate rrna expression
## 453                                        inhibition of dna recombination at telomere
## 789  recognition and association of dna glycosylase with site containing an affected p
## 863                                                          rho gtpases activate pkns
## 1016                                        sirt1 negatively regulates rrna expression
## 610                                  negative epigenetic regulation of rrna expression
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 9               2.398400e-09                        1          6        8
## 76              2.398400e-09                        1          6        8
## 89              2.398400e-09                        1          6        8
## 247             2.398400e-09                        1          6        8
## 293             2.398400e-09                        1          6        8
## 453             2.398400e-09                        1          6        8
## 789             2.398400e-09                        1          6        8
## 863             2.398400e-09                        1          6        8
## 1016            2.398400e-09                        1          6        8
## 610             3.583122e-09                        1          6        9
##               FDR
## 9    2.427823e-07
## 76   2.427823e-07
## 89   2.427823e-07
## 247  2.427823e-07
## 293  2.427823e-07
## 453  2.427823e-07
## 789  2.427823e-07
## 863  2.427823e-07
## 1016 2.427823e-07
## 610  2.427823e-07
## 
## [1] "set_33"
##  [1] "OSBPL6"   "PDE4D"    "RALGPS2"  "RFC3"     "PIGK"     "MAGI1"   
##  [7] "PTPN14"   "SETBP1"   "TIAM1"    "PLEKHA7"  "ATAD5"    "DNAH14"  
## [13] "WWC3"     "PLEKHA5"  "PDE4A"    "CUX2"     "RLF"      "ESYT2"   
## [19] "DENND1A"  "MAPK8IP1" "STARD13"  "AGAP3"    "DENND4C"  "WDR45B"  
## [25] "RIT2"     "SRSF12"   "AGAP1"    "FAM110B"  "ROBO1"    "TANC2"   
## [31] "FAM20C"   "CADM1"    "PDE4B"    "SIPA1L1"  "RGL3"    
## $reactome
##            category over_represented_pvalue under_represented_pvalue numDEInCat
## 203 darpp 32 events            2.703721e-05                        1          3
##     numInCat        FDR
## 203        3 0.03195798
## 
## [1] "set_38"
##  [1] "SNCAIP"  "RPH3A"   "LRRC74A" "MEIS1"   "RORA"    "RAB27A"  "SMARCD3"
##  [8] "CELF4"   "TBL1X"   "NPDC1"   "EPHA4"   "AKT3"    "EMILIN2" "DRAM1"  
## [15] "KCNH1"   "PAM"     "CLVS2"   "LRRC4C"  "CLEC1A"  "CRIM1"   "PDE3B"  
## [22] "KALRN"   "ZFPM2"   "PPM1E"   "ALOX15B" "ZDHHC20" "UNC5C"   "TSHZ2"  
## [29] "EFNA5"   "NELL2"   "OSBP2"   "PBX1"    "KAZN"    "MIB2"    "MICAL3" 
## [36] "GRIN2B" 
## $reactome
##                           category over_represented_pvalue
## 899 rora activates gene expression            2.099059e-05
##     under_represented_pvalue numDEInCat numInCat        FDR
## 899                        1          3        3 0.02481088
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8955030 478.3   16112782 860.6         NA 16112782 860.6
## Vcells 16666630 127.2   31295163 238.8      65536 31295163 238.8
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] goseq_1.50.0           geneLenDataBase_1.34.0 BiasedUrn_2.0.10      
##  [4] fgsea_1.24.0           biomaRt_2.54.1         limma_3.54.2          
##  [7] tidyr_1.3.0            ggpubr_0.6.0           ggplot2_3.4.2         
## [10] data.table_1.14.8     
## 
## loaded via a namespace (and not attached):
##   [1] nlme_3.1-162                matrixStats_1.0.0          
##   [3] bitops_1.0-7                bit64_4.0.5                
##   [5] filelock_1.0.2              progress_1.2.2             
##   [7] httr_1.4.6                  GenomeInfoDb_1.34.9        
##   [9] tools_4.2.3                 backports_1.4.1            
##  [11] bslib_0.4.2                 utf8_1.2.3                 
##  [13] R6_2.5.1                    mgcv_1.8-42                
##  [15] DBI_1.1.3                   BiocGenerics_0.44.0        
##  [17] colorspace_2.1-0            withr_2.5.0                
##  [19] tidyselect_1.2.0            prettyunits_1.1.1          
##  [21] bit_4.0.5                   curl_5.0.1                 
##  [23] compiler_4.2.3              cli_3.6.1                  
##  [25] Biobase_2.58.0              xml2_1.3.4                 
##  [27] DelayedArray_0.24.0         rtracklayer_1.58.0         
##  [29] sass_0.4.5                  scales_1.2.1               
##  [31] rappdirs_0.3.3              Rsamtools_2.14.0           
##  [33] stringr_1.5.0               digest_0.6.31              
##  [35] rmarkdown_2.21              XVector_0.38.0             
##  [37] pkgconfig_2.0.3             htmltools_0.5.5            
##  [39] MatrixGenerics_1.10.0       dbplyr_2.3.2               
##  [41] fastmap_1.1.1               rlang_1.1.0                
##  [43] rstudioapi_0.14             RSQLite_2.3.1              
##  [45] BiocIO_1.8.0                jquerylib_0.1.4            
##  [47] generics_0.1.3              jsonlite_1.8.4             
##  [49] BiocParallel_1.32.6         dplyr_1.1.2                
##  [51] car_3.1-2                   RCurl_1.98-1.12            
##  [53] magrittr_2.0.3              GO.db_3.16.0               
##  [55] GenomeInfoDbData_1.2.9      Matrix_1.6-4               
##  [57] Rcpp_1.0.10                 munsell_0.5.0              
##  [59] S4Vectors_0.36.2            fansi_1.0.4                
##  [61] abind_1.4-5                 lifecycle_1.0.3            
##  [63] stringi_1.7.12              yaml_2.3.7                 
##  [65] carData_3.0-5               SummarizedExperiment_1.28.0
##  [67] zlibbioc_1.44.0             org.Hs.eg.db_3.16.0        
##  [69] BiocFileCache_2.6.1         grid_4.2.3                 
##  [71] blob_1.2.4                  parallel_4.2.3             
##  [73] crayon_1.5.2                lattice_0.20-45            
##  [75] splines_4.2.3               Biostrings_2.66.0          
##  [77] cowplot_1.1.1               GenomicFeatures_1.50.4     
##  [79] hms_1.1.3                   KEGGREST_1.38.0            
##  [81] knitr_1.44                  pillar_1.9.0               
##  [83] GenomicRanges_1.50.2        rjson_0.2.21               
##  [85] ggsignif_0.6.4              codetools_0.2-19           
##  [87] stats4_4.2.3                fastmatch_1.1-3            
##  [89] XML_3.99-0.14               glue_1.6.2                 
##  [91] evaluate_0.20               png_0.1-8                  
##  [93] vctrs_0.6.2                 gtable_0.3.3               
##  [95] purrr_1.0.1                 cachem_1.0.7               
##  [97] xfun_0.39                   broom_1.0.4                
##  [99] restfulr_0.0.15             rstatix_0.7.2              
## [101] tibble_3.2.1                GenomicAlignments_1.34.1   
## [103] AnnotationDbi_1.60.2        memoise_2.0.1              
## [105] IRanges_2.32.0